Background: The emergence and re-emergence of infectious diseases are a major concern in Public Health. The unique socio-demographic aspects of the Autonomous Community of Madrid make it necessary for a greater deal of attention to be paid to pet-transmitted zoonoses. This study is aimed as heightening the knowledge of the emerging and re-emerging pet-transmitted zoonoses and the design of a method for prioritizing the same. Methods: Based on the diseases obtained from official sources, laboratories and a review of published studies, a quantification and weighting method designed by the working group and adapted to the specificity of this study was applied. Results: Based on the analysis of 137 diseases, 24 met the admission requirements. The weighting method is provided in table form, including eleven scoring criteria, the criteria categories and the coefficients employed. Salmonellosis was the top-ranked disease, followed by Q Fever, Tularemia and Hantavirus Infection. Conclusions: A method for specifically evaluating emerging and re-emerging diseases was designed, affording the possibility of setting priorities in the Public Health planning field. This study provides a listing of 24 zoonoses ranked in order of importance, based on which new strategy-related lines must be set out for the research and/or control thereof.